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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
7d68269 Thomas Mooney 30 March 2015, 22:00:11 UTC Use the "references" variable instead of the original argument list. 30 March 2015, 22:00:11 UTC
62de67b Thomas Mooney 30 March 2015, 18:28:31 UTC Narrow down choices of convertible references by preferring an input. 30 March 2015, 18:28:31 UTC
06d184c Nathaniel Nutter 28 March 2015, 18:09:22 UTC Merge pull request #596 from nnutter/master use canonpath to normalize $test_dir 28 March 2015, 18:09:22 UTC
f5dde25 Nathaniel Nutter 27 March 2015, 22:11:22 UTC use canonpath to normalize $test_dir Use canonpath to normalize path as something in StreamGraph seemed to do the same. For example, `./WorkflowBuilder` becomes just `WorkflowBuilder` which was breaking the full test suite. 27 March 2015, 22:11:22 UTC
17421ed Allison Penner Regier 27 March 2015, 18:32:03 UTC Merge pull request #593 from apregier/shortcut_adaptor Add shortcut to adaptor class 27 March 2015, 18:32:03 UTC
f09043c apregier 27 March 2015, 17:54:11 UTC Shortcut delegates to execute 27 March 2015, 17:54:11 UTC
c44ea31 Allison Penner Regier 27 March 2015, 14:34:09 UTC Merge pull request #546 from apregier/compare_vcf_in_process Compare vcf in process 27 March 2015, 14:34:09 UTC
bfe3ddb apregier 27 March 2015, 01:37:22 UTC Add shortcut to adaptor class There is no reason why this should ever need to run with lots of resources 27 March 2015, 01:38:22 UTC
eab32f6 Thomas B. Mooney 26 March 2015, 21:37:33 UTC Merge pull request #586 from tmooney/remove_unused_properties_from_composite_workflow Remove disused properties. 26 March 2015, 21:37:33 UTC
76f1a76 Thomas B. Mooney 26 March 2015, 21:37:15 UTC Merge pull request #585 from tmooney/dont_log_rollbacks_on_build_requested Don't log rollbacks on build requested 26 March 2015, 21:37:15 UTC
5ccc6a2 Ian Ferguson 26 March 2015, 20:55:18 UTC Merge pull request #573 from iferguson90/picard-class-fix Picard classnames 26 March 2015, 20:55:18 UTC
df7702f Eddie Belter 26 March 2015, 19:41:21 UTC Merge pull request #590 from ebelter/instdata2 InstData Import: give default value to resolved instdata properties 26 March 2015, 19:41:21 UTC
2352f4c Eddie Belter 26 March 2015, 19:40:57 UTC Merge pull request #584 from ebelter/instdata-description InstData Import: pass description on to created instdasta 26 March 2015, 19:40:57 UTC
a828d62 apregier 26 March 2015, 19:39:08 UTC Simplify by passing arguments straight through 26 March 2015, 19:39:08 UTC
ab60abc Nathaniel Nutter 26 March 2015, 19:37:44 UTC Merge pull request #591 from nnutter/master make StreamGraph.t independent of current working directory 26 March 2015, 19:37:44 UTC
8b314a0 Avinash Ramu 26 March 2015, 19:27:44 UTC Merge pull request #547 from gatoravi/clinseq_update_analysis clinseq: update defaults in update-analysis 26 March 2015, 19:27:44 UTC
cdbf64b Ian Ferguson 26 March 2015, 18:48:32 UTC Use an HTTP request instead of a socket 26 March 2015, 18:48:32 UTC
9ab9c24 Avinash Ramu 26 March 2015, 16:27:35 UTC pull in snapshot changes from master 26 March 2015, 16:27:35 UTC
46a7998 Avinash Ramu 26 March 2015, 15:36:17 UTC Merge remote-tracking branch 'origin' into clinseq_update_analysis 26 March 2015, 15:36:17 UTC
e34a533 Avinash Ramu 26 March 2015, 15:33:39 UTC update db snapshot 26 March 2015, 15:33:39 UTC
ad3ab9b Thomas Mooney 26 March 2015, 13:29:14 UTC Replace caller with Carp::shortmess. 26 March 2015, 13:29:14 UTC
edc004b APipe Tester 26 March 2015, 12:16:55 UTC Updated `genome` tab completion. 26 March 2015, 12:16:55 UTC
66f9153 APipe Tester 26 March 2015, 12:15:07 UTC Updated class browser cache. 26 March 2015, 12:15:07 UTC
05f3b91 Ian Ferguson 25 March 2015, 20:17:42 UTC Collect call info and send it to my workstation 25 March 2015, 20:17:42 UTC
0b9c64d Ian Ferguson 25 March 2015, 19:57:14 UTC Don't die when supplied with an undef Picard vers. 25 March 2015, 19:57:14 UTC
1393ae4 Nathaniel Nutter 25 March 2015, 19:30:21 UTC make StreamGraph.t independent of current working directory 25 March 2015, 19:30:21 UTC
ea96bf9 Eddie Belter 25 March 2015, 18:30:35 UTC InstData Import: give default value to resolved instdata properties 25 March 2015, 18:30:35 UTC
c3b5255 Eddie Belter 25 March 2015, 17:13:02 UTC InstData Import: spell cprrect 25 March 2015, 17:13:02 UTC
d2781f2 Susanna Siebert 25 March 2015, 17:10:57 UTC Merge pull request #587 from susannasiebert/alignment_result Filter out G::ID::AlignmentResult 25 March 2015, 17:10:57 UTC
cb14972 Thomas B. Mooney 25 March 2015, 17:00:04 UTC Merge pull request #581 from tmooney/optional_tag_during_add_menu_item Optionally add tag(s) when associating menu item(s) to the AnP. 25 March 2015, 17:00:04 UTC
3017e52 Susanna Siebert 25 March 2015, 13:41:30 UTC Filter out G::ID::AlignmentResult Since per-lane alignments are now G::ID::AlignedBamResult they need to be explicitly filtered out 25 March 2015, 13:41:30 UTC
a9a456b Thomas B. Mooney 25 March 2015, 13:29:12 UTC Merge pull request #579 from tmooney/merge_error_message_on_deleted_object Don't call error_message on a deleted object. 25 March 2015, 13:29:12 UTC
321cd84 Thomas Mooney 25 March 2015, 13:26:52 UTC Remove disused properties. 25 March 2015, 13:26:52 UTC
ea3c493 Thomas Mooney 25 March 2015, 13:09:25 UTC Remove old comments. * We already do have a note. * This isn't especially TGI-specific. 25 March 2015, 13:09:25 UTC
e941937 Thomas Mooney 25 March 2015, 13:04:16 UTC Remove the caller check; make the "real" property _build_requested 25 March 2015, 13:04:16 UTC
2be018e Thomas B. Mooney 24 March 2015, 22:02:39 UTC Merge pull request #577 from tmooney/more_consistent_bases_warnings Don't Warn about Each Missing ".bases" File if We Didn't Make Any 24 March 2015, 22:02:39 UTC
97fbed8 Thomas Mooney 24 March 2015, 21:39:46 UTC Also unlock if our change was rolled back. 24 March 2015, 21:39:46 UTC
b7ce6a3 Thomas Mooney 24 March 2015, 21:38:24 UTC When rolling back, don't lock or record a note. * We don't need to lock, since we're not changing the value. * We don't need to record a note, since the note of the original change will be removed. 24 March 2015, 21:38:24 UTC
47caba6 apregier 24 March 2015, 20:39:50 UTC igv xml file has urls that will be different for each run 24 March 2015, 20:39:50 UTC
3ef7af6 Eddie Belter 24 March 2015, 20:16:38 UTC InstData Import: pass description on to created instdasta 24 March 2015, 20:16:38 UTC
b6ceff1 APipe Tester 24 March 2015, 19:19:53 UTC updated workflow submodule to 0b9e071 24 March 2015, 19:19:53 UTC
4efdf7e Ian Ferguson 24 March 2015, 19:15:34 UTC Add Picard version to Bwamem.t 24 March 2015, 19:15:34 UTC
afb33c8 Ian Ferguson 24 March 2015, 19:03:43 UTC Die when explicitly given an undef Picard version 24 March 2015, 19:03:43 UTC
b045a2c APipe Tester 24 March 2015, 16:25:08 UTC updated workflow submodule to 297de2d 24 March 2015, 16:25:08 UTC
2cdbdd0 Susanna Siebert 24 March 2015, 15:59:02 UTC Merge pull request #576 from susannasiebert/alignment_result Make AlignmentResult an AlignedBamResult 24 March 2015, 15:59:02 UTC
328aa5d Allison Penner Regier 24 March 2015, 15:51:52 UTC Merge pull request #556 from apregier/qc_framework Qc framework 24 March 2015, 15:51:52 UTC
d2fa606 Thomas Mooney 24 March 2015, 14:09:16 UTC Optionally add tag(s) when associating menu item(s) to the AnP. 24 March 2015, 14:09:16 UTC
2fdc12b Susanna Siebert 24 March 2015, 13:18:12 UTC use skip blog instead of commenting out test 24 March 2015, 13:18:12 UTC
4831163 Thomas Mooney 24 March 2015, 13:09:28 UTC Don't call error_message on a deleted object. The rollback will have rolled back our creation. 24 March 2015, 13:09:28 UTC
cbe7dfe Thomas Mooney 23 March 2015, 20:52:11 UTC Create the manifest file before the final reallocation. 23 March 2015, 20:52:11 UTC
63e27c6 Thomas Mooney 23 March 2015, 20:50:30 UTC Only warn about missing bases files if we should have made them. 23 March 2015, 20:50:30 UTC
e90a574 Ian Ferguson 23 March 2015, 20:19:17 UTC Fix version conditional in CompareSams _java_class 23 March 2015, 20:19:17 UTC
50d5e01 Ian Ferguson 23 March 2015, 20:18:07 UTC Add convenience methods around version_compare 23 March 2015, 20:18:58 UTC
8af797f apregier 23 March 2015, 20:16:22 UTC Changed number of arguments b/c not an object method 23 March 2015, 20:16:22 UTC
4428283 apregier 23 March 2015, 19:52:08 UTC Fix how special functions hash is generated 23 March 2015, 19:52:08 UTC
d44ef78 Thomas B. Mooney 23 March 2015, 19:26:18 UTC Merge pull request #530 from tmooney/print_useful_message_on_fl_update Print the display name for blessed objects. 23 March 2015, 19:26:18 UTC
352472d apregier 23 March 2015, 19:06:51 UTC Merge branch 'qc_framework' of github.com:apregier/genome into fireteam 23 March 2015, 19:06:51 UTC
c4bf1ba apregier 23 March 2015, 19:05:56 UTC New streamgraph version fixes cluttered error files 23 March 2015, 19:05:56 UTC
bbae1c5 Susanna Siebert 23 March 2015, 18:24:50 UTC Overwrite AlignedBamResult accessors in AlignmentResult 23 March 2015, 18:24:50 UTC
65db9ac Susanna Siebert 23 March 2015, 18:00:02 UTC Write failing tests for AlignedBamResult accessors 23 March 2015, 18:24:13 UTC
93e7166 Susanna Siebert 23 March 2015, 17:59:36 UTC AlignmentResult is an AlignedBamResult 23 March 2015, 17:59:36 UTC
6b69487 apregier 23 March 2015, 17:09:40 UTC Compare functions should return 0 if files are the same. The old-style diff functions return 1 if the files are the same. 23 March 2015, 17:09:40 UTC
d4a17ef apregier 23 March 2015, 16:16:39 UTC Use proper quoting for regexes 23 March 2015, 16:16:39 UTC
fb73f4d David Morton 23 March 2015, 16:05:03 UTC Merge pull request #575 from mkiwala/initial-ptero-integration Initial ptero integration 23 March 2015, 16:05:03 UTC
fef2364 Allison Penner Regier 23 March 2015, 15:59:03 UTC Merge pull request #4 from tmooney/qc_tool_takes_alignedbamresult QC Tool now takes AlignedBamResult to match QC Run. 23 March 2015, 15:59:03 UTC
c05d89c Michael J. Kiwala 23 March 2015, 15:14:56 UTC Do not compare "user" lines from the resulting json 23 March 2015, 15:14:56 UTC
d63f541 Thomas Mooney 23 March 2015, 14:40:37 UTC QC Tool now takes AlignedBamResult to match QC Run. 23 March 2015, 14:45:25 UTC
a98a522 Michael J. Kiwala 23 March 2015, 14:32:52 UTC Make call to WfBuilder execute() compatible with new function signature 23 March 2015, 14:32:52 UTC
59d8f85 Michael J. Kiwala 23 March 2015, 14:12:13 UTC Remove useless check for empty GENOME_ env var GENOME_WORKFLOW_BUILDER_BACKEND already has a default specified in Env::GENOME_WORKFLOW_BUILDER_BACKEND. 23 March 2015, 14:12:13 UTC
04b0296 Michael J. Kiwala 23 March 2015, 14:11:21 UTC Replace access of $ENV{USER} with call to Genome::Sys->username 23 March 2015, 14:11:21 UTC
1ff49a6 APipe Tester 22 March 2015, 12:18:32 UTC Updated `gmt` tab completion. 22 March 2015, 12:18:32 UTC
2cf8e41 APipe Tester 22 March 2015, 12:17:32 UTC Updated `genome` tab completion. 22 March 2015, 12:17:32 UTC
3a1dae1 David Morton 19 March 2015, 02:03:58 UTC error_message natively supports sprintf formatting 20 March 2015, 18:38:21 UTC
73ce1b6 Michael J. Kiwala 17 March 2015, 19:51:56 UTC Change Carp::confess to die Conflicts: lib/perl/Genome/WorkflowBuilder/DAG.pm 20 March 2015, 18:38:08 UTC
370ae33 Michael J. Kiwala 17 March 2015, 19:45:26 UTC Make requires reference the specific Ptero modules needed 20 March 2015, 18:38:03 UTC
4dde6e0 David Morton 19 March 2015, 01:59:45 UTC Allow WorkflowBuilder to submit to PTero 20 March 2015, 18:37:42 UTC
5c6b82f apregier 20 March 2015, 18:24:40 UTC Update install path 20 March 2015, 18:25:13 UTC
cbdac0a David Morton 19 March 2015, 01:14:24 UTC Allow for multiple WorkflowBuilder backends The interface for the 'execute' method changes here as well. The old interface was to accept any number of named arguments, but this makes it so that the interface cannot be extended in the future. If one were to ever want to add an optional argument to execute, it would collide with the workflow inputs. 20 March 2015, 18:22:38 UTC
4356fd5 Indraniel 20 March 2015, 15:55:48 UTC Merge pull request #568 from indraniel/ercc-map-unaligned-experiment-pt2 ERCC-based Quality Control Screening for RNASeq: Part 2 20 March 2015, 15:55:48 UTC
b968c86 Indraniel Das 20 March 2015, 15:38:48 UTC + make "% Mapped" be a real percentage - the number should be from [0,1], but rather [0, 100]. 20 March 2015, 15:38:48 UTC
0527802 APipe Tester 20 March 2015, 12:20:08 UTC Updated `gmt` tab completion. 20 March 2015, 12:20:08 UTC
1850df5 APipe Tester 20 March 2015, 12:19:05 UTC Updated `genome` tab completion. 20 March 2015, 12:19:05 UTC
b699197 APipe Tester 20 March 2015, 12:16:36 UTC Updated class browser cache. 20 March 2015, 12:16:36 UTC
8fc9d7a Thomas B. Mooney 19 March 2015, 22:09:43 UTC Merge pull request #572 from tmooney/less_stratospheric_memory_limits Match -M to actual resource requests. 19 March 2015, 22:09:43 UTC
da48ab3 Indraniel Das 19 March 2015, 20:43:02 UTC + fix p-value Mix label typo 19 March 2015, 20:43:02 UTC
89048b0 Indraniel Das 19 March 2015, 20:08:38 UTC + use the genome allocated version of the ERCC_Controls_Analysis.txt - this currently the advised way to handle this file 19 March 2015, 20:08:38 UTC
68872bb Indraniel Das 19 March 2015, 19:48:52 UTC + apply @jasonwalker80 's 4th recommendation (PR 568) - Jason mention to show the ERCC re-alignment statistics in the outputs. See comment in BIO-1345. 19 March 2015, 19:53:15 UTC
34b3fde Indraniel Das 19 March 2015, 19:45:51 UTC + let generate_idxstats return the file not data hash - let the 'generate_tsvfile' method get the data hash elements. This is for a refactoring to introduce alignment statistics in the outputs. See the next commit about it. 19 March 2015, 19:53:14 UTC
0c1f9e2 Indraniel Das 18 March 2015, 23:59:59 UTC + apply @jasonwalker80 's 3rd recommendation (PR 568) - refine the outputs of the R Script: include the results of the statistical tests applied - Highlight what the automated system thinks the mixture is via the "DECISION: " line. - refine what message gets outputted when the automated system has trouble making a decision. - Adjust the output formatting into sections ("Tables", "Tests", & "Plots). - See comment in BIO-1345. 19 March 2015, 19:52:57 UTC
067e9c5 Indraniel Das 18 March 2015, 23:19:16 UTC + apply @jasonwalker80 's 2nd recommendation (PR 568) - change the "Probability" column name to "ExpectedMixRatios" This is a better term for the end users. See comment in BIO-1345. 19 March 2015, 19:52:39 UTC
ea07844 Indraniel Das 18 March 2015, 23:15:27 UTC + apply @jasonwalker80 's 1st recommendation (PR 568) - use a reference sequence that's recorded in the genome system. This is the same ERCC reference sequence as before, but has been appended to an existing imported reference sequence. 19 March 2015, 19:52:09 UTC
062c46c Avinash Ramu 19 March 2015, 15:57:08 UTC Merge pull request #531 from gatoravi/somaticfilter_workflow somatic-filter workflow 19 March 2015, 15:57:08 UTC
841f4ce Thomas B. Mooney 19 March 2015, 15:16:48 UTC Merge pull request #569 from tmooney/harmonize_dv2_dispatcher_resources Set tmp and mem requests for DV2 dispatchers 19 March 2015, 15:16:48 UTC
84947b1 Thomas B. Mooney 19 March 2015, 15:09:19 UTC Merge pull request #570 from tmooney/lower_false_indel_memory_requests Lower false indel memory requests 19 March 2015, 15:09:19 UTC
af3292f apregier 19 March 2015, 02:23:22 UTC Make Builds rely on comparer for file comparisons 19 March 2015, 02:23:22 UTC
a8c0746 apregier 19 March 2015, 02:22:26 UTC Move comparer to base class 19 March 2015, 02:22:26 UTC
94fb67f apregier 19 March 2015, 02:13:41 UTC Don't cache comparer as ur property If the process object is used as an input, ur will freak out because it has code refs in one of its properties 19 March 2015, 02:13:41 UTC
821951c Indraniel Das 18 March 2015, 23:04:58 UTC + reapply @acoffman 's earlier suggestion - somehow I lost @acoffman's original file existence modifications from an earlier commit. Perhaps it got "Lost in Refactoring". 18 March 2015, 23:04:58 UTC
059ccfd apregier 18 March 2015, 21:53:31 UTC Enforce abstract class 18 March 2015, 21:53:31 UTC
e8c10ad Ian Ferguson 18 March 2015, 21:37:12 UTC Prepend 'net.sf' to class for Picard < 1.114 18 March 2015, 21:45:56 UTC
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